The developmental dynamics of the Populus stem transcriptome

doi:10.1111/pbi.12958

CORC > 植物研究所 > 中国科学院植物研究所 > 中科院光生物学重点实验室

	The developmental dynamics of the Populus stem transcriptome
	Chao, Qing ; Gao, Zhi-Fang ; Zhang, Dong 5; Zhao, Biligen-Gaowa ; Dong, Feng-Qin ; Fu, Chun-Xiang ; Liu, Li-Jun ; Wang, Bai-Chen
刊名	PLANT BIOTECHNOLOGY JOURNAL
	2019
卷号	17 期号:1 页码:206-219
关键词	PacBio Iso-Seq stem cell maintenance primary growth secondary growth transcription factor
ISSN号	1467-7644
DOI	10.1111/pbi.12958
文献子类	Article
英文摘要	The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.
学科主题	Biotechnology & Applied Microbiology ; Plant Sciences
电子版国际标准刊号	1467-7652
出版地	HOBOKEN
WOS关键词	SHOOT APICAL MERISTEM ; LONG NONCODING RNAS ; SECONDARY GROWTH ; WOOD FORMATION ; CELL-DIFFERENTIATION ; ARABIDOPSIS GENE ; DNA METHYLATION ; WALL SYNTHESIS ; PLANT ; ROOT
WOS研究方向	Biotechnology & Applied Microbiology ; Plant Sciences
语种	英语
出版者	WILEY
WOS记录号	WOS:000455486500018
资助机构	National High Technology Research and Development Program of ChinaNational High Technology Research and Development Program of China [2013AA102701]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/19572]
专题	中科院光生物学重点实验室
作者单位	1.Biomarker Technol Corp, Beijing, Peoples R China 2.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing, Peoples R China 3.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao Engn Res Ctr Biomass Resources & Environm, Key Lab Biofuels, Qingdao, Shandong, Peoples R China 4.Shandong Agr Univ, Coll Forestry, Tai An, Shandong, Peoples R China 5.Univ Chinese Acad Sci, Beijing, Peoples R China 6.Chinese Acad Sci, Inst Bot, Photosynth Res Ctr, Key Lab Photobiol, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Chao, Qing,Gao, Zhi-Fang,Zhang, Dong,et al. The developmental dynamics of the Populus stem transcriptome[J]. PLANT BIOTECHNOLOGY JOURNAL,2019,17(1):206-219.
APA	Chao, Qing.,Gao, Zhi-Fang.,Zhang, Dong.,Zhao, Biligen-Gaowa.,Dong, Feng-Qin.,...&Wang, Bai-Chen.(2019).The developmental dynamics of the Populus stem transcriptome.PLANT BIOTECHNOLOGY JOURNAL,17(1),206-219.
MLA	Chao, Qing,et al."The developmental dynamics of the Populus stem transcriptome".PLANT BIOTECHNOLOGY JOURNAL 17.1(2019):206-219.